Joss-reviews: [PRE REVIEW]: MicrobiomeR: An R Package for Simplified and Standardized Microbiome Analysis Workflows
Submitting author: @grabear (Robert Gilmore)
Repository: https://github.com/vallenderlab/MicrobiomeR
Version: 0.5.1
Editor: @lpantano
Reviewers: @CosteaPaul
Author instructions
Thanks for submitting your paper to JOSS @grabear. Currently, there isn't an JOSS editor assigned to your paper.
@grabear if you have any suggestions for potential reviewers then please mention them here in this thread. In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission.
Editor instructions
The JOSS submission bot @whedon is here to help you find and assign reviewers and start the main review. To find out what @whedon can do for you type:
@whedon commands
whedon
All 98 comments
Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.
For a list of things I can do to help you, just type:
@whedon commands
What happens now?
This submission is currently in a pre-review state which means we are waiting for an editor to be assigned and for them to find some reviewers for your submission. This may take anything between a few hours to a couple of weeks. Thanks for your patience :smile_cat:
You can help the editor by looking at this list of potential reviewers to identify individuals who might be able to review your submission (please start at the bottom of the list). Also, feel free to suggest individuals who are not on this list by mentioning their GitHub handles here.
whedon
on 28 Feb 2019
Attempting PDF compilation. Reticulating splines etc...
PDF failed to compile for issue #1288 with the following error:
/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in block in find': No such file or directory - tmp/1288 (Errno::ENOENT)
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:incollect!'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in find'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-01ece1d1d135/lib/whedon/processor.rb:57:infind_paper_paths'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-01ece1d1d135/bin/whedon:50:in prepare'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:inrun'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:indispatch'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-01ece1d1d135/bin/whedon:116:inload'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in
whedon
on 28 Feb 2019
👋 @pjotrp - the author requested you (or someone from your group) as editor - ok?
Of course, some work is needed on the paper first...
danielskatz
on 28 Feb 2019
👋 @grabear - I don't see the paper part of your submission. Take a look at the author submission guidelines, specifically What should my paper contain? and Example paper and bibliography
danielskatz
on 28 Feb 2019
Hi, I put the paper in a separate folder under inst/paper/ @danielskatz
grabear
on 28 Feb 2019
@whedon generate pdf from inst/paper
danielskatz
on 28 Feb 2019
Attempting PDF compilation. Reticulating splines etc...
thanks - I see some issues with the figure, the table, and the references. You can make changes to the paper.md and paper.bib, then use the same command I used (as a new comment here) to regenerate until you are satisfied with the generated proof.
danielskatz
on 28 Feb 2019
In the meantime, @pjotrp and his group can figure out who will edit this, I think.
danielskatz
on 28 Feb 2019
@danielskatz Thank you! I'll work on it.
grabear
on 28 Feb 2019
@whedon commands
grabear
on 28 Feb 2019
Here are some things you can ask me to do:
# List Whedon's capabilities
@whedon commands
# List of editor GitHub usernames
@whedon list editors
# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers
EDITORIAL TASKS
# Compile the paper
@whedon generate pdf
# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name
# Ask Whedon to check the references for missing DOIs
@whedon check references
@whedon generate pdf from branch joss-review from inst/paper
grabear
on 28 Feb 2019
Attempting PDF compilation from custom branch joss-review from inst/paper . Reticulating splines etc...
@sdhutchins working on tweaking the paper!
grabear
on 28 Feb 2019
Yes, I'll ask for an editor.
pjotrp
on 28 Feb 2019
@whedon assign @lpantano as editor
lpantano
on 1 Mar 2019
OK, the editor is @lpantano
whedon
on 1 Mar 2019
@whedon generate pdf from inst/paper branch joss-review
grabear
on 1 Mar 2019
Attempting PDF compilation. Reticulating splines etc...
Hi @grabear,
let me know when you can figure out the format issue, I will look into possible reviewers in the meantime.
Looking forward to working together in the process.
Cheers
lpantano
on 1 Mar 2019
Hello @lpantano! I'll be working on it this afternoon! I just need to play around with whedon a little.
Looking forward to it as well :+1:
grabear
on 1 Mar 2019
@whedon generate pdf from branch joss-review inst/paper
grabear
on 1 Mar 2019
Attempting PDF compilation from custom branch joss-review inst/paper. Reticulating splines etc...
@pjotrp @lpantano @danielskatz Any idea what I should do with @whedon when I'm generating the pdf on a separate branch and in a folder that's not on the top level?
grabear
on 1 Mar 2019
👋 @arfon ?
danielskatz
on 1 Mar 2019
Part of the problem is that I always protect my master and dev-master branches, so it makes it a bit more complicated for me to edit. I can always change the permissions temporarily, but that's not ideal.
grabear
on 1 Mar 2019
@whedon generate pdf from branch joss-review
grabear
on 1 Mar 2019
Attempting PDF compilation from custom branch joss-review. Reticulating splines etc...
sorry @grabear that is not working with two of the conditions (other branch and other location), hopefully, somebody who knows the backend infrastructure can help. I will reach somebody if @arfon doesn't chime in.
At least the figure now. seems right. :)
Thanks!
lpantano
on 1 Mar 2019
@lpantano It seems to be working now! It's finding the paper, so no complaints. :)
grabear
on 1 Mar 2019
@whedon generate pdf from branch joss-review
grabear
on 1 Mar 2019
Attempting PDF compilation from custom branch joss-review. Reticulating splines etc...
@whedon check references
grabear
on 1 Mar 2019
Attempting to check references...
```Reference check summary:
OK DOIs
MISSING DOIs
- https://doi.org/10.1371/journal.pone.0061217 may be missing for title: phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data
- https://doi.org/10.1038/nmeth.f.303 may be missing for title: QIIME allows analysis of high-throughput community sequencing data.
- https://doi.org/10.1093/nar/gks1219 may be missing for title: The SILVA ribosomal RNA gene database project: improved data processing and web-based tools.
- https://doi.org/10.1093/nar/gkt1209 may be missing for title: The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks.
INVALID DOIs
- None
```
whedon
on 1 Mar 2019
@whedon check references from branch joss-review
grabear
on 1 Mar 2019
Attempting to check references...
```Reference check summary:
OK DOIs
MISSING DOIs
- https://doi.org/10.1371/journal.pone.0061217 may be missing for title: phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data
- https://doi.org/10.1038/nmeth.f.303 may be missing for title: QIIME allows analysis of high-throughput community sequencing data.
- https://doi.org/10.1093/nar/gks1219 may be missing for title: The SILVA ribosomal RNA gene database project: improved data processing and web-based tools.
- https://doi.org/10.1093/nar/gkt1209 may be missing for title: The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks.
INVALID DOIs
- None
```
whedon
on 1 Mar 2019
@whedon generate pdf from branch joss-review
grabear
on 1 Mar 2019
Attempting PDF compilation from custom branch joss-review. Reticulating splines etc...
@whedon generate pdf from branch joss-review
grabear
on 1 Mar 2019
Attempting PDF compilation from custom branch joss-review. Reticulating splines etc...
PDF failed to compile for issue #1288 with the following error:
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 16 0 16 0 0 207 0 --:--:-- --:--:-- --:--:-- 207
Error producing PDF.
! Misplaced \noalign.
\hline ->\noalign
{\ifnum 0=`}\fi \hrule @height \arrayrulewidth \futurelet...
l.386 \hline
Looks like we failed to compile the PDF
whedon
on 1 Mar 2019
@whedon generate pdf from branch joss-review
grabear
on 2 Mar 2019
Attempting PDF compilation from custom branch joss-review. Reticulating splines etc...
@whedon generate pdf from branch joss-review
grabear
on 2 Mar 2019
Attempting PDF compilation from custom branch joss-review. Reticulating splines etc...
@whedon generate pdf from branch joss-review
grabear
on 2 Mar 2019
Attempting PDF compilation from custom branch joss-review. Reticulating splines etc...
@lpantano @sdhutchins I think I have the table, diagram, and DOIs in a good place.
Thoughts?
grabear
on 2 Mar 2019
Thanks!
I think looks good, the only think is that some DOIs have the https and other not. Can you normalize that?
lpantano
on 2 Mar 2019
Hi @CosteaPaul,
@brainstorm mentioned to me that you could be a good reviewer for this paper, Do you think you would have time for this? It would be great!
lpantano
on 2 Mar 2019
I think it looks good, @grabear! I would only say perhaps the diagram's height could be decreased while keeping the same scale. It looks good as it is though.
sdhutchins
on 2 Mar 2019
@whedon generate pdf from branch joss-review
grabear
on 2 Mar 2019
Attempting PDF compilation from custom branch joss-review. Reticulating splines etc...
@whedon generate pdf from branch joss-review
grabear
on 4 Mar 2019
Attempting PDF compilation from custom branch joss-review. Reticulating splines etc...
@whedon generate pdf from branch joss-review
grabear
on 4 Mar 2019
Attempting PDF compilation from custom branch joss-review. Reticulating splines etc...
@lpantano @sdhutchins Made some changes!
grabear
on 4 Mar 2019
@whedon check references
grabear
on 4 Mar 2019
Attempting to check references...
```Reference check summary:
OK DOIs
MISSING DOIs
- https://doi.org/10.1371/journal.pone.0061217 may be missing for title: phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data
- https://doi.org/10.1038/nmeth.f.303 may be missing for title: QIIME allows analysis of high-throughput community sequencing data.
- https://doi.org/10.1093/nar/gks1219 may be missing for title: The SILVA ribosomal RNA gene database project: improved data processing and web-based tools.
- https://doi.org/10.1093/nar/gkt1209 may be missing for title: The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks.
INVALID DOIs
- None
```
whedon
on 4 Mar 2019
@lpantano this looks like fun :).
Would be happy to help with reviewing, though I have no idea how this is supposed to work.
CosteaPaul
on 4 Mar 2019
Thank you, @CosteaPaul !
We have some guidelines here:
https://joss.readthedocs.io/en/latest/reviewer_guidelines.html
For now, I will move this to review, that will close this issue and open a new one where the review process will happen. Our friend whedon, will help you with the requirements to review the paper. When the new issue is open, there will be some guidelines. I will follow up there.
Thanks so much!
lpantano
on 4 Mar 2019
@whedon assign @CosteaPaul as reviewer
lpantano
on 4 Mar 2019
OK, the reviewer is @CosteaPaul
whedon
on 4 Mar 2019
Hi @grabear,
I see there are some issues with the DOI links , let me know when you solve this and we can move this to under review.
Thanks!
lpantano
on 4 Mar 2019
@lpantano All of those DOI's are not missing. I copied an pasted those during my first check, so Idk why they are considered "Missing" or "may be missing".
I just updated an F1000 DOI, but only because they release a second version of that paper. I also checked all of the other ones and they are working links..
grabear
on 4 Mar 2019
Hi,
Weird, When I click on the PDF link it lands on a broken web page. Did you try to use the link of the PDF, maybe there is something wrong on the latex code that breaks the link?
https://doi.org/https://doi.org/10.1038/nmeth.f.303 This url is malformed.
Cheers
lpantano
on 4 Mar 2019
@whedon generate pdf from branch joss-review
grabear
on 4 Mar 2019
Attempting PDF compilation from custom branch joss-review. Reticulating splines etc...
@whedon check references
grabear
on 5 Mar 2019
Attempting to check references...
```Reference check summary:
OK DOIs
MISSING DOIs
- https://doi.org/10.1371/journal.pone.0061217 may be missing for title: phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data
- https://doi.org/10.1038/nmeth.f.303 may be missing for title: QIIME allows analysis of high-throughput community sequencing data.
- https://doi.org/10.1093/nar/gks1219 may be missing for title: The SILVA ribosomal RNA gene database project: improved data processing and web-based tools.
- https://doi.org/10.1093/nar/gkt1209 may be missing for title: The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks.
INVALID DOIs
- None
```
whedon
on 5 Mar 2019
@whedon check references from branch joss-review
grabear
on 5 Mar 2019
Attempting to check references...
```Reference check summary:
OK DOIs
MISSING DOIs
- https://doi.org/10.1371/journal.pone.0061217 may be missing for title: phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data
- https://doi.org/10.1038/nmeth.f.303 may be missing for title: QIIME allows analysis of high-throughput community sequencing data.
- https://doi.org/10.1093/nar/gks1219 may be missing for title: The SILVA ribosomal RNA gene database project: improved data processing and web-based tools.
- https://doi.org/10.1093/nar/gkt1209 may be missing for title: The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks.
INVALID DOIs
- None
```
whedon
on 5 Mar 2019
Not really sure what's going on with whedon's reference check, but the DOIs should be correct now. Sorry about that!
grabear
on 5 Mar 2019
@whedon check references from branch joss-review
I'm afraid @whedon only knows how to check references for the master or default branch of your repository.
arfon
on 5 Mar 2019
Thank you, @arfon. I think is fine since the links work now. I will start the review process.
@whedon start review
lpantano
on 5 Mar 2019
Whedon needs separate lines
pjotrp
on 5 Mar 2019
@whedon start review
pjotrp
on 5 Mar 2019
OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/1299. Feel free to close this issue now!
whedon
on 5 Mar 2019
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Most helpful comment
In the meantime, @pjotrp and his group can figure out who will edit this, I think.